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stacomiR (version 0.6.1)

Fish Migration Monitoring

Description

Graphical outputs and treatment for a database of fish pass monitoring. It is a part of the 'STACOMI' open source project developed in France by the French Office for Biodiversity institute to centralize data obtained by fish pass monitoring. This version is available in French and English. See for more information on 'STACOMI'.

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Version

Install

install.packages('stacomiR')

Monthly Downloads

246

Version

0.6.1

License

GPL (>= 2)

Maintainer

Last Published

March 3rd, 2024

Functions in stacomiR (0.6.1)

charge,ref_par-method

Loading method for ref_par referential objects

charge,ref_df-method

Loading method for DF referential objects

Generic method for calculations

charge,ref_env-method

Loading method for ref_env referential object

charge,ref_parqual-method

Loading method for Reparqual referential objects

calcule,report_species-method

calcule method for report_species

charge,ref_choice-method

Loading method for Refchoice referential objects

charge,ref_dc-method

Method to load the counting devices of the control station

charge,ref_coe-method

loads the coefficients for the period defined in class

charge,report_dc-method

charge method for report_dc

charge,ref_year-method

Loading method for ref_year referential objects

charge,report_mig-method

Loads additional data on migration control operations, df (fishway) dc (counting device).

charge,report_env-method

charge method for report_env class

charge,report_df-method

charge method for report_df

charge,report_annual-method

charge method for report_annual class

charge,ref_list-method

Loading method for ref_list referential objects

charge,report_ope-method

charge method for report_ope

charge,ref_stage-method

Loading method for ref_stage referential objects

charge,ref_parquan-method

Loading method for Reparquan referential objects

Generic method to load referentials

charge,report_mig_interannual-method

loading method for report_mig_interannual class

charge,report_sample_char-method

charge method for report_sample_char class

charge,report_species-method

charge method for report_species

charge,report_mig_char-method

charge method for report_mig_char

charge_with_filter,ref_par-method

Loading method for ref_par referential objects searching only those parameters existing for a DC, a Taxa, and a stage

charge_with_filter,ref_parqual-method

Loading method for Reparqual referential objects searching only those parameters existing for a DC, a Taxon, and a stage

charge,report_mig_env-method

charge method for report_mig_env class

charge_complement

Generic method to load additional data

charge_complement,ref_parqual-method

Loads an additional dataset this method is loaded to obtain the possible values of a qualitative parameter. Here data only contains one line

choice_c,ref_par-method

Command line interface to select a parameter

choice_c,ref_dc-method

Command line interface to select a counting device

charge,report_silver_eel-method

charge method for report_silver_eel class

choice_c,ref_choice-method

Choice_c method for ref_choice referential objects

charge,ref_taxa-method

Loading method for ref_taxa referential objects

charge,ref_textbox-method

Loading method for ref_textbox referential objects

charge,report_mig_mult-method

charge method for report_mig_mult

charge_with_filter,ref_stage-method

Loading method for ref_stage referential objects searching only those stages existing for a DC and a Taxon

charge_with_filter,ref_parquan-method

Loading method for Reparquan referential objects searching only those parameters existing for a DC (counting device), a Taxon, and a stage

choice_c,ref_stage-method

choice_c method for ref_stage

charge,report_sea_age-method

Loads data and check that all choices in the graphical interface have been made.

choice_c,ref_env-method

Command line interface to select a monitoring station

choice_c,report_mig_interannual-method

command line interface for report_mig_interannual class

choice_c,ref_df-method

Command line interface to choose a fishway

charge_with_filter,ref_taxa-method

Loading method for ref_taxa referential objects searching only taxa existing for a DC

choice_c,report_mig_char-method

command line interface for report_mig_char class

connect,report_dc-method

connect method for report_dc

choice_c,ref_timestep_daily-method

choice_c method for class ref_timestep_daily

choice_c,report_annual-method

command line interface for report_annual-class

choice_c,ref_year-method

choice_c method for ref_year referential from the command line

choice_c,report_dc-method

command line interface for report_dc class

connect,report_df-method

connect method for report_df

connect,report_mig_env-method

connect method for report_mig_env class

connect,report_mig_interannual-method

connect method for report_mig_interannual

Generic method for manual choice using the command line

Silvering index coefficients from Caroline Durif (2009) to predict silvering stage from morphological parameters

choice_c,report_mig_env-method

command line interface for report_env class

connect,report_species-method

connect method for report_species

connect,report_silver_eel-method

connect method for report_silver_eel

connect,report_mig_mult-method

connect method for report_mig_mult

connect,report_ope-method

connect method for report_ope

choice_c,report_env-method

command line interface for report_env class

choice_c,report_silver_eel-method

command line interface for report_silver_eel class

choice_c,ref_list-method

Choice_c method for ref_list referential objects

choice_c,ref_horodate-method

Choice_c method for ref_horodate

choice_c,report_sea_age-method

command line interface for report_sea_age class

choice_c,ref_taxa-method

choice_c method for ref_taxa

choice_c,report_ge_weight-method

command line interface for report_ge_weight-class

choice_c,report_sample_char-method

command line interface for report_sample_char class

choice_c,report_mig-method

command line interface for report_mig class

choice_c,report_df-method

command line interface for report_df class

charge_with_filter

Generic method to load referentials, with filters from the parent object in the database

choice_c,ref_textbox-method

Choice_c method for ref_textbox referential objects

Builds a table with colors to merge with a dataframe for later use in ggplot. An initial check will be done on the name of the color vector. A data frame is built. It contains a column color which is a factor. The factor order match the order of the vector (not the alphabetical order of the colors).

choice_c,report_species-method

command line interface for report_species-class

fn_connect_report_mig_interannual

Get table content for table t_bilanmigrationjournalier_bjo in report_mig_interannual

Environment where most objects from the package are stored and then loaded by the charge method

fun_report_mig_mult

Calculate daily migration by simple repartition

connect,report_annual-method

connect method for report_annual class this method performs the sum over the year attention this function does not count subsamples.

connect,report_env-method

connect method for report_env class

choice_c,report_mig_mult-method

command line used to build report_mig_mult class

fun_report_mig_mult_overlaps

Function to calculate daily migration using overlaps functions

funplotreport_silver_eel

funplotreport_silver_eel

connect,report_ge_weight-method

connect method for report_Poids_moyen

fun_write_monthly

This writes monthly data in t_reportmensuel_mens table

Internal use barchart for report_df class from the graphical interface

Function to plot calendar like graph, internal use

Function for report_mig graphs including numbers DF DC operations

Generic for prediction

connect,report_mig-method

connect method for report_mig

plot,report_annual,missing-method

Plot method for report_annual

plot,report_mig_mult,missing-method

Plots of various type for report_mig_mult

fun_aggreg_for_plot

Calculates a data.frame where all components within the list calcdata are aggregated and formatted for plot

connect,report_sample_char-method

connect method for report_sample_char

connect,report_mig_char-method

connect method for report_mig_char

Function to calculate statistics per month

end_date,ref_timestep-method

Gets the final horodate for an object of class ref_timestep-class

Generic method for getting the final date

connect,report_sea_age-method

connect method for report_sea_age

plot,report_sample_char,missing-method

Plots of various type for reportcarlot

function used to remove special non utf8 character which cause the gtk interface to crash

Creates a list of available schemas in the db

plot,report_mig_env,missing-method

Plot method for report_mig_env

An object of class report_mig_env with data loaded

Internal use, function used in the graphical interface to create a barchart for report_df class

function used for some lattice graphs with dates

Generic method getvalue

fun_stage_durif

Function to calculate the stages from Durif

Internal use, rectangles to describe the DF work for report_df class,

print,report_mig_mult-method

Method to print the command line of the object

plot,report_mig_interannual,missing-method

Plot method for report_mig_interannual

print,report_sample_char-method

Method to print the command line of the object

this function gets the name of the stucture as it is set in the database

plot,report_dc,missing-method

Different plots for report_dc

fungraph_glasseel

Graph function for glass eel migration. Differs from fungraph as it does not draw the ggplot graph for month

plot,report_df,missing-method

Different plots for report_df

Generic method to get the years

this function displays text and will be used to convey stacomiR message in shiny

get_year,ref_timestep-method

Gets the year or a vector of years corresponding to the timestep ("ref_timestep") object

print,report_mig-method

Method to print the command line of the object

print,report_df-method

Method to print the command line of the object

Video counting of Marine lamprey (Petromyzon marinus) in 2012 in the Vilaine (France)

Silver eel migration in the Somme

this function gets the schema from envir stacomi and throws warning

Anguilla migration at the Arzal station (report_mig_mult-class)

Qualitative and quantitative parameters describing Salmon migration at Decize (Loire)

r_mig_interannual

Daily glass eel and elver migration from 1984 to 2016 in the Sevre Niortaise

r_mig_interannual_vichy

Seasonality of salmon migration at the Vichy counting station (Loire)

Counting device operation for three different counting device in Arzal (Vilaine, France)

Counting device operation for the video recording (Arzal dam, Vilaine, France).

Fishway operation for the vertical slot fishway (Arzal dam, Vilaine, France).

ref_choice-class

Class 'ref_choice'

Class 'ref_env'

fun_weight_conversion

returns a table where weights and number are calculated from number and weights respectively performs a query to collect the conversion coefficients

fun_date_extraction

This function extracts temporal characteristics from a dataframe

fun_report_mig_interannual

statistics per time period

fun_table_per_dis

functions called in DF and DC

function to print and save statistics in .csv and .html formats for report_mig and report_mig_mult class

Table output for report_df class

Internal function, tests the connection and if it works loads the stacomi interface

model,report_ge_weight-method

model method for report_ge_weight' this method uses samples collected over the season to model the variation in weight of glass eel or yellow eels.

plot,report_env,missing-method

Plot method for report_env

ref_timestep-class

Class "ref_timestep"

Class 'ref_coe'

Annual migration of yellow and silver eel for three fishways / counting devices at the Arzal dam (data from 1995 to 2016)

ref_timestepChar-class

Class "ref_timestepChar"

plot,report_mig,ANY-method

Plots of various type for report_mig.

plot,report_ge_weight,missing-method

Plot method for report_ge_weight'

An object of class report_env with data loaded

ref_parquan-class

Class 'ref_parquan'

Fishway operation at the Arzal Dam (Vilaine France) (3 Fishways in 2011)

Annual migration of salmon in the Adour and tributaries

Wet weight of glass eel from the trapping ladder (Arzal, Vilaine France)

print,report_sea_age-method

Method to print the command line of the object

plot,report_silver_eel,missing-method

Plots of various type for report_silver_eel

plot,report_sea_age,missing-method

Plots of various type for report_sea_age

print,report_silver_eel-method

Method to print the command line of the object

Class 'ref_par'

report_species-class

Counts of number per taxa/stages

setasqualitative,report_mig_char-method

Turns a continuous parameter into discrete values

ref_stage-class

Class 'ref_stage'

report_annual-class

Class "report_annual"

report_dc-class

Class "report_dc" report du fonctionnement du dispositif de comptage

ref_horodate-class

Class ref_horodate

summary,report_df-method

summary for report_df, write csv and html output, and prints summary statistics

An object of class report_ope-class with data loaded

report_mig-class

Migration report for one DC, one species and one stage

Counting operations for three different counting device in Arzal (Vilaine, France)

report_ge_weight-class

Trend of wet weight in glass eel

report_df-class

Report on fishway operation

report_silver_eel-class

Class "report_silver_eel"

report_env-class

class report_env simple output of one or several environmental conditions...

ref_parqual-class

Class 'ref_parqual'

summary,report_mig-method

summary for report_mig calls functions funstat and funtable to create migration overviews and generate csv and html output in the user data directory

Year reference class

Class 'ref_list'

ref_timestep_daily-class

Class 'ref_timestep_daily'

report_mig_interannual-class

Class "report_mig_interannual"

report_sea_age-class

Class "report_sea_age"

report_mig_char-class

Migration report along with quantitative and qualitative characteristics

summary,report_species-method

summary for report_species

supprime,report_mig_interannual-method

supprime method for report_mig_interannual class, deletes values in table t_bilanmigrationjournalier_bjo

stacomi Main launcher for program stacomi

summary,report_dc-method

summary for report_dc, write csv and html output, and prints summary statistics

xtable,report_annual-method

xtable function for report_annual-class create an xtable objet but also assigns an add.to.column argument in envir_stacomi, for later use by the print.xtable method.

plot,report_mig_char,missing-method

plot method for report_mig_char

summary,report_mig_char-method

summary for report_mig_char

summary,report_mig_interannual-method

summary for report_mig_interannual provides summary statistics for the latest year (if silent=TRUE), or the year selected in the interface, if silent=FALSE. Mean, min and max are historical statistics and they always include the current year from the historical dataset.

summary,report_sea_age-method

summary for report_sea_age

report_mig_env-class

Class "report_mig_env"

report_mig_mult-class

Migration reports for multiple DC / species / stages

xtable,report_mig_char-method

xtable function for report_mig_char-class create an xtable objet to be later used by the print.xtable method.

supprime,report_sea_age-method

supprime method for report_mig_interannual class

Generic method to delete entires from the database

print,report_dc-method

Method to print the command line of the object.

plot,report_species,missing-method

Plot method for report_species

Validity check for ref_year

validity_ref_horodate

Validity check for ref_horodate

supprime,ref_coe-method

supprime method for 'ref_coe' class

vector_to_listsql

Transforms a vector into a string called within an sql command e.g. c('A','B','C') => in ('A','B','C')

summary,report_silver_eel-method

summary for report_silver_eel

Overview of the fishway operation at Arzal in (Vilaine France).

An object of class report_sea_age with data loaded

Size of yellow and glass eel at the Arzal dam (Vilaine, France) in the fishway and main eel trapping ladder.

Counting Device (DC) operation from 2000 to 2015 at the Arzal dam (Vilaine, France)

ref_textbox-class

ref_textbox referencial class

setasqualitative

Generic method to transform quantitative par into a qualitative one

Create a dataframe suitable for charts per 24h and day

Class 'ref_taxa'

report_ope-class

Report on operations

report_sample_char-class

Class 'report_sample_char'

summary,report_mig_mult-method

summary for report_mig_mult calls functions funstat and funtable to create migration overviews and generate csv and html output in the user data directory

write_database,report_ge_weight-method

Method to write data to the stacomi database for report_ge_weight-class

write_database,report_mig-method

Command line method to write the daily and monthly counts to the t_bilanmigrationjournalier_bjo table

summary,report_sample_char-method

summary for report_sample_char

Generic method write_database

write_database,report_sea_age-method

Command line method to write the characteristic "sea age" (car_par_code='A124') into the tj_caracteristiquelot_car table in the user's scheme

calcule,report_mig_env-method

Calculations for migration in the class report_mig_env-class

calcule,report_mig_interannual-method

calcule method for report_mig_interannual

barplot,report_annual-method

barplot method for object report_annual-class

calcule,report_silver_eel-method

Calculate individual silver eel parameters.

calcule,report_mig_char-method

Computes data to a standard format for the summary and plot methods.

calcule,report_mig-method

Transforms migration per period to daily migrations, and performs the conversion from weights to number is data are stored as weights (glass eel).

calcule,report_sea_age-method

Split data according to the limits set in the limit1hm, and limit2hm arguments of the report_sea_age-class.

calcule,report_mig_mult-method

#' Transforms migration per period to daily migrations, and performs the conversion from weights to number is data are stored as weights (glass eel). This calculation is performed in a loop for all dc.

calcule,report_ge_weight-method

Calcule method for report_ge_weight

calcule,report_sample_char-method

Calculation for report_sample_char